We have SNP data from 30 fungal isolates from which we can filter for non-synonymous SNPs (using SnpEff). We also have a binary coding system which indicates the presence/absence of specific cognate R(esistance) genes in the host plant for each of those 30 isolates (essentially giving avirulence/avirulence phenotypes for each fungal isolate on the host plant). Is it possible to screen the SNP data across the isolates for those SNPs potentially linked to effector genes specific to the gene-for-gene interaction?
I have experience with NGS processing software as well as Perl/Python/R scripting but am new to the gene association field. Is what I describe above conceptually feasible? If so I would greatly appreciate any advice on how to carry this out and/or what software to use. I would be happy to supply more specific information should it be needed. I hope I've been reasonably clear explaining our situation.
Thanks in advance, R.